diff --git a/gtsam/basis/ParameterMatrix.h b/gtsam/basis/ParameterMatrix.h
index eddcbfeae..7fa99ac62 100644
--- a/gtsam/basis/ParameterMatrix.h
+++ b/gtsam/basis/ParameterMatrix.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file ParamaterMatrix.h
+ * @file ParameterMatrix.h
  * @brief Define ParameterMatrix class which is used to store values at
  * interpolation points.
  * @author Varun Agrawal, Frank Dellaert
diff --git a/gtsam/geometry/Cal3_S2Stereo.h b/gtsam/geometry/Cal3_S2Stereo.h
index ae0052fd5..ad66b53ff 100644
--- a/gtsam/geometry/Cal3_S2Stereo.h
+++ b/gtsam/geometry/Cal3_S2Stereo.h
@@ -38,7 +38,7 @@ class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
   using shared_ptr = boost::shared_ptr<Cal3_S2Stereo>;
 
   /// @name Standard Constructors
-  /// @
+  /// @{
 
   /// default calibration leaves coordinates unchanged
   Cal3_S2Stereo() = default;
@@ -55,6 +55,8 @@ class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
   Cal3_S2Stereo(double fov, int w, int h, double b)
       : Cal3_S2(fov, w, h), b_(b) {}
 
+  /// @}
+
   /**
    * Convert intrinsic coordinates xy to image coordinates uv, fixed derivaitves
    * @param p point in intrinsic coordinates
@@ -82,7 +84,6 @@ class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
    */
   Vector3 calibrate(const Vector3& p) const { return Cal3_S2::calibrate(p); }
 
-  /// @}
   /// @name Testable
   /// @{
 
diff --git a/gtsam/geometry/OrientedPlane3.h b/gtsam/geometry/OrientedPlane3.h
index d2ad4230e..92d167379 100644
--- a/gtsam/geometry/OrientedPlane3.h
+++ b/gtsam/geometry/OrientedPlane3.h
@@ -133,8 +133,6 @@ public:
   inline double distance() const {
     return d_;
   }
-
-  /// @}
 };
 
 template<> struct traits<OrientedPlane3> : public internal::Manifold<
diff --git a/gtsam/geometry/Pose3.cpp b/gtsam/geometry/Pose3.cpp
index 2938e90f5..2652fc073 100644
--- a/gtsam/geometry/Pose3.cpp
+++ b/gtsam/geometry/Pose3.cpp
@@ -27,7 +27,6 @@
 namespace gtsam {
 
 using std::vector;
-using Point3Pairs = vector<Point3Pair>;
 
 /** instantiate concept checks */
 GTSAM_CONCEPT_POSE_INST(Pose3)
diff --git a/gtsam/geometry/Pose3.h b/gtsam/geometry/Pose3.h
index 33fb55250..711829425 100644
--- a/gtsam/geometry/Pose3.h
+++ b/gtsam/geometry/Pose3.h
@@ -83,7 +83,7 @@ public:
    *  A pose aTb is estimated between pairs (a_point, b_point) such that a_point = aTb * b_point
    *  Note this allows for noise on the points but in that case the mapping will not be exact.
    */
-  static boost::optional<Pose3> Align(const std::vector<Point3Pair>& abPointPairs);
+  static boost::optional<Pose3> Align(const Point3Pairs& abPointPairs);
 
   // Version of Pose3::Align that takes 2 matrices.
   static boost::optional<Pose3> Align(const Matrix& a, const Matrix& b);
diff --git a/gtsam/geometry/Similarity2.h b/gtsam/geometry/Similarity2.h
index 05f10d149..c02a20a65 100644
--- a/gtsam/geometry/Similarity2.h
+++ b/gtsam/geometry/Similarity2.h
@@ -132,7 +132,7 @@ class GTSAM_EXPORT Similarity2 : public LieGroup<Similarity2, 4> {
    * using the algorithm described here:
    * http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2005/Zinsser05-PSR.pdf
    */
-  static Similarity2 Align(const std::vector<Pose2Pair>& abPosePairs);
+  static Similarity2 Align(const Pose2Pairs& abPosePairs);
 
   /// @}
   /// @name Lie Group
diff --git a/gtsam/geometry/Similarity3.h b/gtsam/geometry/Similarity3.h
index 845d4c810..f3b07e63c 100644
--- a/gtsam/geometry/Similarity3.h
+++ b/gtsam/geometry/Similarity3.h
@@ -120,7 +120,7 @@ class GTSAM_EXPORT Similarity3 : public LieGroup<Similarity3, 7> {
   /**
    *  Create Similarity3 by aligning at least three point pairs
    */
-  static Similarity3 Align(const std::vector<Point3Pair>& abPointPairs);
+  static Similarity3 Align(const Point3Pairs& abPointPairs);
 
   /**
    * Create the Similarity3 object that aligns at least two pose pairs.
diff --git a/gtsam/geometry/SphericalCamera.h b/gtsam/geometry/SphericalCamera.h
index 4880423d3..dc9e4bbde 100644
--- a/gtsam/geometry/SphericalCamera.h
+++ b/gtsam/geometry/SphericalCamera.h
@@ -82,7 +82,6 @@ class GTSAM_EXPORT SphericalCamera {
   EmptyCal::shared_ptr emptyCal_;
 
  public:
-  /// @}
   /// @name Standard Constructors
   /// @{
 
diff --git a/gtsam/hybrid/HybridGaussianFactorGraph.h b/gtsam/hybrid/HybridGaussianFactorGraph.h
index 0188aa652..6dc9cd409 100644
--- a/gtsam/hybrid/HybridGaussianFactorGraph.h
+++ b/gtsam/hybrid/HybridGaussianFactorGraph.h
@@ -106,13 +106,13 @@ class GTSAM_EXPORT HybridGaussianFactorGraph
   void add(JacobianFactor&& factor);
 
   /// Add a Jacobian factor as a shared ptr.
-  void add(boost::shared_ptr<JacobianFactor> factor);
+  void add(JacobianFactor::shared_ptr factor);
 
   /// Add a DecisionTreeFactor to the factor graph.
   void add(DecisionTreeFactor&& factor);
 
   /// Add a DecisionTreeFactor as a shared ptr.
-  void add(boost::shared_ptr<DecisionTreeFactor> factor);
+  void add(DecisionTreeFactor::shared_ptr factor);
 };
 
 }  // namespace gtsam
diff --git a/gtsam/inference/BayesTree-inst.h b/gtsam/inference/BayesTree-inst.h
index b341c1d5a..82899b299 100644
--- a/gtsam/inference/BayesTree-inst.h
+++ b/gtsam/inference/BayesTree-inst.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file    BayesTree-inl.h
+ * @file    BayesTree-inst.h
  * @brief   Bayes Tree is a tree of cliques of a Bayes Chain
  * @author  Frank Dellaert
  * @author  Michael Kaess
diff --git a/gtsam/inference/ClusterTree-inst.h b/gtsam/inference/ClusterTree-inst.h
index 9bc141955..6295549c4 100644
--- a/gtsam/inference/ClusterTree-inst.h
+++ b/gtsam/inference/ClusterTree-inst.h
@@ -1,5 +1,5 @@
 /**
- * @file EliminatableClusterTree-inst.h
+ * @file ClusterTree-inst.h
  * @date Oct 8, 2013
  * @author Kai Ni
  * @author Richard Roberts
diff --git a/gtsam/inference/ClusterTree.h b/gtsam/inference/ClusterTree.h
index 7dd414193..26c853a7b 100644
--- a/gtsam/inference/ClusterTree.h
+++ b/gtsam/inference/ClusterTree.h
@@ -1,5 +1,5 @@
 /**
- * @file EliminatableClusterTree.h
+ * @file ClusterTree.h
  * @date Oct 8, 2013
  * @author Kai Ni
  * @author Richard Roberts
@@ -139,7 +139,6 @@ class ClusterTree {
              const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
 
   /// @}
-
   /// @name Advanced Interface
   /// @{
 
@@ -169,6 +168,7 @@ class ClusterTree {
 
  protected:
   /// @name Details
+  /// @{
 
   /// Assignment operator - makes a deep copy of the tree structure, but only pointers to factors
   /// are copied, factors are not cloned.
@@ -236,6 +236,7 @@ class EliminatableClusterTree : public ClusterTree<GRAPH> {
 
  protected:
   /// @name Details
+  /// @{
 
   /// Assignment operator - makes a deep copy of the tree structure, but only pointers to factors
   /// are copied, factors are not cloned.
diff --git a/gtsam/inference/EliminationTree-inst.h b/gtsam/inference/EliminationTree-inst.h
index b8d446e49..ea79c9b55 100644
--- a/gtsam/inference/EliminationTree-inst.h
+++ b/gtsam/inference/EliminationTree-inst.h
@@ -10,7 +10,7 @@
 * -------------------------------------------------------------------------- */
 
 /**
-* @file    EliminationTree-inl.h
+* @file    EliminationTree-inst.h
 * @author  Frank Dellaert
 * @author  Richard Roberts
 * @date    Oct 13, 2010
diff --git a/gtsam/inference/FactorGraph-inst.h b/gtsam/inference/FactorGraph-inst.h
index a2ae07101..d6c1d5d8a 100644
--- a/gtsam/inference/FactorGraph-inst.h
+++ b/gtsam/inference/FactorGraph-inst.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file   FactorGraph-inl.h
+ * @file   FactorGraph-inst.h
  * @brief  Factor Graph Base Class
  * @author Carlos Nieto
  * @author Frank Dellaert
diff --git a/gtsam/inference/ISAM-inst.h b/gtsam/inference/ISAM-inst.h
index 1c183b70f..39d840906 100644
--- a/gtsam/inference/ISAM-inst.h
+++ b/gtsam/inference/ISAM-inst.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file    ISAM-inl.h
+ * @file    ISAM-inst.h
  * @brief   Incremental update functionality (iSAM) for BayesTree.
  * @author  Michael Kaess
  */
diff --git a/gtsam/inference/Ordering.h b/gtsam/inference/Ordering.h
index b366b3b3a..97d5bf110 100644
--- a/gtsam/inference/Ordering.h
+++ b/gtsam/inference/Ordering.h
@@ -89,7 +89,8 @@ public:
    */
   FastMap<Key, size_t> invert() const;
 
-  /// @name Fill-reducing Orderings @{
+  /// @name Fill-reducing Orderings
+  /// @{
 
   /// Compute a fill-reducing ordering using COLAMD from a factor graph (see details for note on
   /// performance). This internally builds a VariableIndex so if you already have a VariableIndex,
@@ -215,7 +216,8 @@ public:
 
   /// @}
 
-  /// @name Named Constructors @{
+  /// @name Named Constructors
+  /// @{
 
   template<class FACTOR_GRAPH>
   static Ordering Create(OrderingType orderingType,
@@ -241,7 +243,8 @@ public:
 
   /// @}
 
-  /// @name Testable @{
+  /// @name Testable
+  /// @{
 
   GTSAM_EXPORT
   void print(const std::string& str = "", const KeyFormatter& keyFormatter =
diff --git a/gtsam/navigation/AttitudeFactor.h b/gtsam/navigation/AttitudeFactor.h
index 3016b31af..490c8b17f 100644
--- a/gtsam/navigation/AttitudeFactor.h
+++ b/gtsam/navigation/AttitudeFactor.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- *  @file   Pose3AttitudeFactor.h
+ *  @file   AttitudeFactor.h
  *  @author Frank Dellaert
  *  @brief  Header file for Attitude factor
  *  @date   January 28, 2014
diff --git a/gtsam/navigation/ImuBias.h b/gtsam/navigation/ImuBias.h
index 9346a4a77..a023a38c1 100644
--- a/gtsam/navigation/ImuBias.h
+++ b/gtsam/navigation/ImuBias.h
@@ -36,6 +36,9 @@ public:
   /// dimension of the variable - used to autodetect sizes
   static const size_t dimension = 6;
 
+  /// @name Standard Constructors
+  /// @{
+
   ConstantBias() :
       biasAcc_(0.0, 0.0, 0.0), biasGyro_(0.0, 0.0, 0.0) {
   }
@@ -48,6 +51,8 @@ public:
       biasAcc_(v.head<3>()), biasGyro_(v.tail<3>()) {
   }
 
+  /// @}
+
   /** return the accelerometer and gyro biases in a single vector */
   Vector6 vector() const {
     Vector6 v;
@@ -83,7 +88,6 @@ public:
     return measurement - biasGyro_;
   }
 
-  /// @}
   /// @name Testable
   /// @{
 
diff --git a/gtsam/nonlinear/NonlinearISAM.cpp b/gtsam/nonlinear/NonlinearISAM.cpp
index 512069a8a..840712eb6 100644
--- a/gtsam/nonlinear/NonlinearISAM.cpp
+++ b/gtsam/nonlinear/NonlinearISAM.cpp
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file NonlinearISAM-inl.h
+ * @file NonlinearISAM.cpp
  * @date Jan 19, 2010
  * @author Viorela Ila and Richard Roberts
  */
diff --git a/gtsam/slam/BetweenFactor.h b/gtsam/slam/BetweenFactor.h
index fc1dc4481..5422a61ec 100644
--- a/gtsam/slam/BetweenFactor.h
+++ b/gtsam/slam/BetweenFactor.h
@@ -59,6 +59,9 @@ namespace gtsam {
     // shorthand for a smart pointer to a factor
     typedef typename boost::shared_ptr<BetweenFactor> shared_ptr;
 
+    /// @name Standard Constructors
+    /// @{
+
     /** default constructor - only use for serialization */
     BetweenFactor() {}
 
@@ -68,6 +71,8 @@ namespace gtsam {
       Base(model, key1, key2), measured_(measured) {
     }
 
+    /// @}
+
     ~BetweenFactor() override {}
 
     /// @return a deep copy of this factor
@@ -75,7 +80,6 @@ namespace gtsam {
       return boost::static_pointer_cast<gtsam::NonlinearFactor>(
           gtsam::NonlinearFactor::shared_ptr(new This(*this))); }
 
-    /// @}
     /// @name Testable
     /// @{
 
diff --git a/gtsam/slam/SmartFactorParams.h b/gtsam/slam/SmartFactorParams.h
index e8a1fa7ab..4f23c085d 100644
--- a/gtsam/slam/SmartFactorParams.h
+++ b/gtsam/slam/SmartFactorParams.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file   SmartFactorParams
+ * @file   SmartFactorParams.h
  * @brief  Collect common parameters for SmartProjection and SmartStereoProjection factors
  * @author Luca Carlone
  * @author Zsolt Kira
diff --git a/gtsam/slam/StereoFactor.h b/gtsam/slam/StereoFactor.h
index b2fdbf7a4..40ea7158f 100644
--- a/gtsam/slam/StereoFactor.h
+++ b/gtsam/slam/StereoFactor.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file    GenericStereoFactor.h
+ * @file    StereoFactor.h
  * @brief   A non-linear factor for stereo measurements
  * @author  Alireza Fathi
  * @author  Chris Beall
diff --git a/gtsam/symbolic/SymbolicConditional.h b/gtsam/symbolic/SymbolicConditional.h
index 3abec92b8..4f4917950 100644
--- a/gtsam/symbolic/SymbolicConditional.h
+++ b/gtsam/symbolic/SymbolicConditional.h
@@ -103,6 +103,7 @@ namespace gtsam {
     /// @}
 
     /// @name Testable
+    /// @{
 
     /** Print with optional formatter */
     void print(
diff --git a/gtsam_unstable/geometry/BearingS2.h b/gtsam_unstable/geometry/BearingS2.h
index 197d4910d..59819c555 100644
--- a/gtsam_unstable/geometry/BearingS2.h
+++ b/gtsam_unstable/geometry/BearingS2.h
@@ -22,7 +22,8 @@ protected:
 public:
   static const size_t dimension = 2;
 
-  // constructors
+  /// @name Constructors
+  /// @{
 
   /** Default constructor - straight ahead */
   BearingS2() {}
diff --git a/gtsam_unstable/geometry/Event.cpp b/gtsam_unstable/geometry/Event.cpp
index 45a24c101..1262823da 100644
--- a/gtsam_unstable/geometry/Event.cpp
+++ b/gtsam_unstable/geometry/Event.cpp
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- *  @file  Event
+ *  @file  Event.cpp
  *  @brief Space-time event
  *  @author Frank Dellaert
  *  @author Jay Chakravarty
diff --git a/gtsam_unstable/geometry/Event.h b/gtsam_unstable/geometry/Event.h
index 383c34915..ddeda180e 100644
--- a/gtsam_unstable/geometry/Event.h
+++ b/gtsam_unstable/geometry/Event.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- *  @file  Event
+ *  @file  Event.h
  *  @brief Space-time event
  *  @author Frank Dellaert
  *  @author Jay Chakravarty
diff --git a/gtsam_unstable/linear/QPSParser.cpp b/gtsam_unstable/linear/QPSParser.cpp
index c755f2451..44e24e0b0 100644
--- a/gtsam_unstable/linear/QPSParser.cpp
+++ b/gtsam_unstable/linear/QPSParser.cpp
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file     QPParser.cpp
+ * @file     QPSParser.cpp
  * @author   Ivan Dario Jimenez
  * @date     3/5/16
  */
diff --git a/gtsam_unstable/linear/QPSParser.h b/gtsam_unstable/linear/QPSParser.h
index 088168829..bd4254d0f 100644
--- a/gtsam_unstable/linear/QPSParser.h
+++ b/gtsam_unstable/linear/QPSParser.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file     QPParser.h
+ * @file     QPSParser.h
  * @brief    QPS parser implementation
  * @author   Ivan Dario Jimenez
  * @date     3/5/16
diff --git a/gtsam_unstable/slam/Mechanization_bRn2.cpp b/gtsam_unstable/slam/Mechanization_bRn2.cpp
index 6112a398f..0bb1085a0 100644
--- a/gtsam_unstable/slam/Mechanization_bRn2.cpp
+++ b/gtsam_unstable/slam/Mechanization_bRn2.cpp
@@ -1,5 +1,5 @@
 /**
- * @file Mechanization_bRn.cpp
+ * @file Mechanization_bRn2.cpp
  * @date Jan 25, 2012
  * @author Chris Beall
  * @author Frank Dellaert
diff --git a/gtsam_unstable/slam/Mechanization_bRn2.h b/gtsam_unstable/slam/Mechanization_bRn2.h
index 5a6f1df6d..4714f2b6f 100644
--- a/gtsam_unstable/slam/Mechanization_bRn2.h
+++ b/gtsam_unstable/slam/Mechanization_bRn2.h
@@ -1,5 +1,5 @@
 /**
- * @file Mechanization_bRn.h
+ * @file Mechanization_bRn2.h
  * @date Jan 25, 2012
  * @author Chris Beall
  * @author Frank Dellaert
diff --git a/gtsam_unstable/slam/PoseToPointFactor.h b/gtsam_unstable/slam/PoseToPointFactor.h
index 071d13aec..2f8bad6df 100644
--- a/gtsam_unstable/slam/PoseToPointFactor.h
+++ b/gtsam_unstable/slam/PoseToPointFactor.h
@@ -1,5 +1,5 @@
 /**
- *  @file   PoseToPointFactor.hpp
+ *  @file   PoseToPointFactor.h
  *  @brief  This factor can be used to model relative position measurements
  *  from a (2D or 3D) pose to a landmark
  *  @author David Wisth